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Could someone please clarify what is protein secondary structure: https://en.wikipedia.org/wiki/Protein_secondary_structure

I believe I understand the primary structure, I am not sure what's the difference between secondary and tertiary structure. Tertiary structure seems to be 3d structure of a polypeptide but I am not at all clear about the secondary structure.

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    $\begingroup$ Can you clarify your question? what do you know about protein secondary structure and what are you having a hard time understanding? $\endgroup$ – De Novo Jul 10 '18 at 20:33
  • $\begingroup$ @DanHall I am studying the structure of protein and while I believe I understand the primary structure, I am not sure what's the difference between secondary and tertiary structure. Tertiary structure seems to be 3d structure of a polypeptide but I am not at all clear about the secondary structure. Does this help? $\endgroup$ – erudite Jul 10 '18 at 20:39
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    $\begingroup$ edit your question to include that :) $\endgroup$ – De Novo Jul 10 '18 at 20:57
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Proteins are made up of long chains of amino acids covalently joined together. The order of amino acids is the primary structure of a protein. In physiologic conditions, these long chains of amino acids fold into three dimensional shapes. The terms secondary and tertiary structure are used to refer to specific aspects of the three dimensional shape.

tl;dr what's the difference?

Both secondary and tertiary structure refer to the three-dimensional shape of a protein. Secondary structure is the regular repeating patterns, generally stabilized by hydrogen bonds between the NH and CO groups of the peptide backbone. Tertiary structure can be thought of as the way secondary structural elements fold together to create the overall shape of the protein.

Secondary structure

Secondary structure refers to regular repeating patterns stabilized by hydrogen bonding between the NH and CO groups of the peptide bond. Typically textbooks will focus on the $\alpha$-helix and the $\beta$-sheet.

Berg biochemistry has some useful diagrams demonstrating these secondary structures. The first is an $\alpha$-helix. The side-chains are represented by green balls here. Notice the orientation of the NH and CO groups, which stabilize this structure:

enter image description here

The $\beta$-sheet forms a very different secondary structure, but it's also stabilized by hydrogen bonding between NH and CO groups of the peptide bond.

enter image description here

Tertiary structure

Tertiary structure is the larger three-dimensional structure of a protein in its environment. It can be useful to think of tertiary structure as the way different secondary structural elements fold together to form the full, active protein. Notice in this figure, also from Berg, the way the elements of secondary structure (the $\alpha$-helices) fold into an overall three dimensional shape that can nicely cradle the heme group.

enter image description here

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Secondary structure proteins are repeating chains of alpha helixes and beta sheets like spider silk. Tertiary structure proteins are globular proteins, like enzymes.

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  • $\begingroup$ All proteins have both secondary and tertiary structure in physiologic conditions. These terms do not refer to different proteins. They refer to different aspects of their structure. $\endgroup$ – De Novo Jul 11 '18 at 0:52

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